10-1308893-T-C

Variant names:

• chr10-1308893-T-C
• rs1007147
• NM_018702.4:c.1078-37824A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.1078-37824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,120 control chromosomes in the GnomAD database, including 16,350 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (16350 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 5 publications found

Genes affected

ADARB2 (HGNC:227): (adenosine deaminase RNA specific B2 (inactive)) This gene encodes a member of the double-stranded RNA adenosine deaminase family of RNA-editing enzymes and may play a regulatory role in RNA editing. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1078-37824A>G		intron_variant	Intron 3 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1078-37824A>G		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67009 AN: 152002 Hom.: 16346 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.441 AC: 67027 AN: 152120 Hom.: 16350 Cov.: 32 AF XY: 0.446 AC XY: 33164 AN XY: 74340

African (AFR) AF: 0.230 AC: 9564 AN: 41520

American (AMR) AF: 0.525 AC: 8034 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3559 AN: 5176

South Asian (SAS) AF: 0.689 AC: 3324 AN: 4822

European-Finnish (FIN) AF: 0.461 AC: 4865 AN: 10558

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34230 AN: 67966

Other (OTH) AF: 0.465 AC: 982 AN: 2110

Alfa AF: 0.484 Hom.: 7226

Bravo AF: 0.432

Asia WGS AF: 0.663 AC: 2304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.53
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1007147; hg19: chr10-1351088;